The Origin Of The Feces

IRA FLATOW: This is Science Friday. I’m Ira Flatow. The fossil record is littered with countless interesting things. Ancient bones of giant beasts, the remains of long extinct plant life, to name a couple. For some researchers, though, nothing is more exciting than finding fossilized feces. Yes, you heard me right.

Dr. Christina Warriner is in this camp. She’s an assistant professor of anthropology at Harvard University. Sci-fi producer Kathleen Davis spoke to Dr. Warriner about her recent research with fossilized feces.

KATHLEEN DAVIS: These ancient poops are called coprolites. And they’re pretty rare. The origins might be less than glamorous, but each one is a gold mine of information about who left it behind. And that’s because coprolites are a snapshot of the microbiome from which they came. Some researchers say studying these ancient records of diet and bacteria that helped us learn about modern problems like lactose intolerance and inflammation.

Dr. Christina Warriner, thanks so much for joining us on Science Friday.

CHRISTINA WARINNER: Thank you for having me.

KATHLEEN DAVIS: I want to start with a technical question. People and animals make waste constantly. And at the same time, we’re not drowning in coprolites. What makes them so uncommon?

CHRISTINA WARINNER: Well, fortunately, most feces does break down and compost really, really quickly. Otherwise, we’d be swimming in it at this point. But no, they do preserve archaeologically under very specific conditions. And generally, we only find preserved feces when you have something that immobilizes water. So that could be a very, very dry environment that desiccates the material or really salty soils or freezing, for example.

KATHLEEN DAVIS: Mm-hmm. So does that mean that the coprolites that we do have are often found in the same places?

CHRISTINA WARINNER: Exactly. They almost always come from some sort of context that’s extremely dry or frozen. So places like dry caves in the American southwest or in northern Mexico, or salty deposits in mountainous areas. Those are typically where we find coprolites.

KATHLEEN DAVIS: And so, say you have a coprolite in front of you that you want to study. What kind of information can you actually learn from it?

CHRISTINA WARINNER: Well, although we tend to just flush it away without thinking about it, they’re actually incredibly rich sources of information about ourselves, about our lives, and about our activities. So for example, our feces contain our own DNA. So you can reconstruct a person’s genome from a fecal sample.

They also are a great snapshot of our gut microbiome, where we can understand the structure of the microbiome, the types of bacteria that are present. We can look for evidence of infection. So pathogens, either bacterial pathogens or potentially viral pathogens. We can also look for things like parasites, which were very common in the past.

And then, of course, we also have dietary DNA that’s present. And this can provide a real important window into what people eat in the past.

KATHLEEN DAVIS: Mm-hmm. And remind us again what the microbiome is.

CHRISTINA WARINNER: So the microbiome is this community of bacteria that lives in and on the human body. And they’re very important. For a long time, they were very difficult to study. And so we really underestimated their importance. But we now realize they’re a fundamental part of our biology. And we actually rely on many of their activities for basic biological functions. Everything ranging from digestion to even producing some of the vitamins that we require.

KATHLEEN DAVIS: So I would assume that to be fossilized these coprolites would have to be pretty old. I mean, how much detail is actually retained inside of them?

CHRISTINA WARINNER: Well, it really depends on the preservation. So sometimes, they actually resemble turds, and they’re very visibly recognizable. Other times, they’ve been really squashed and flattened by the sediments around them. And so you can look at them visually and often identify them as coprolites. They have a different texture and consistency than the soil around them.

But that doesn’t necessarily mean that they’re preserved at a molecular level. So many of them, although they retain some aspects of their morphology or shape, have actually essentially composted in place and have been replaced by soil bacteria. But rarely, we do find these extraordinarily well preserved coprolites. These particular cases where they’ve dried out very, very fast.

And in those cases, they still retain the original bacteria the original human DNA and the original dietary DNA. Those are the ones we’re trying to focus on.

KATHLEEN DAVIS: You recently studied a problem that apparently plagues coprolite researchers. Human coprolites can be confused with those from other species. How does that happen?

CHRISTINA WARINNER: So to some degree, I was aware that this could happen. But I wasn’t aware of the scale of it until we started digging into this problem a little bit more closely. So feces turned up at archaeological sites in different contexts.

Actually, toilets are really rare in the archaeological record. Most people either deposited fecal material into what we call mittens or garbage deposits or practiced open defecation. So any systematic sewage treatment or collection is actually not that common archaeologically. We do find, then, these feces mixed in with different– usually garbage at different sites. In dry caves, in particular. And we had assumed– many people had assumed for a long time that the vast majority of this was human.

However, over time, there have been a number of cases that really raise suspicion as to whether or not some of this truly was human or not. Now, some types of feces are really easy to distinguish. So cow pie is very obvious. It’s huge and it contains very fibrous material and grasses that cows eat, for example.

But dogs are a bit different. Dogs have lived with humans for tens of thousands of years. They poop in the same places. And so you could mix these up. Now, from fresh feces, you can often distinguish human and dog feces just on the basis of size or shape. But archaeologically, those features often get very distorted just through the formation of the archaeological site. So the compression of sediments around them, the color changes as the pigments inside the feces breakdown.

And so many of those visual cues you might use to identify dog feces just aren’t present in the archaeological record. Because they co-occur, and because dogs are often fed by humans. So they ate the same food. And so microscopically, they contain the same food material. They can be really hard to distinguish.

KATHLEEN DAVIS: I think anyone listening to this who has a dog or has cleaned up after a dog before is going to have a very visceral reaction to this conversation. So how do you actually distinguish the human coprolites from the dog ones?

CHRISTINA WARINNER: So there are some techniques that can be used microscopically. Dogs do get infected with different types of parasites, for example. And dogs who are feral dogs will often hunt rodents, for example. And so you’ll find little rodent bones in their feces.

However, for dogs that are really associated with humans and being fed by humans, we have to take another approach. And so here we used genomics to solve this problem. But we had to use two different approaches. Because one of the big problems we face in the archaeological record is that, for many ancient people, dogs were a major and important food. So dogs were consumed as food.

So you might expect to find dog DNA in human feces. And also dogs, very frequently, will scavenge either human latrines or open defecation sites for human feces. And so you might expect to find some human DNA in dog feces. So as a first pass, we did look at the abundance of either dog DNA or human DNA from the feces, but we didn’t feel that was sufficient to really distinguish them.

So we took it to a second level and we looked at the microbial communities as well. And the microbial communities within the human gut microbiome and the dog gut microbiome, although similar in many ways, are distinct. And so we were able to use these two different lines of evidence to distinguish them.

KATHLEEN DAVIS: And what was the age range of the coprolites that you were looking at in this study?

CHRISTINA WARINNER: So the oldest ones we looked at date to around 7,000 years ago and come from Neolithic China. The youngest ones that we looked at are actually just a few centuries old and come from Surrey, England. Where we had a really unusual case where there was a house that was constructed in the 18th century. And someone had taken a chamber pot that had a turd in it and walled it up into the house.

And it was only discovered in the 1990s when the homeowners were renovating. And so when they took down the walls and opened up the attic, they found this chamber pot. And so we thought this must be a clear case of human feces because what else would you find in a chamber pot, although it is very odd that it’s in a wall.

But that turned out to be a dog, actually. So it’s an enduring mystery as to what the story is behind that case.

KATHLEEN DAVIS: That is very strange. Did you learn anything about the humans that were the source of the coprolites during this study?

CHRISTINA WARINNER: Yeah, so we didn’t actually set out to find dog feces. The ancient dog poop. We started the study, really, because we were interested in the humans themselves, and then discovered that we had dogs mixed in.

But what we’re really after with this study is we’re trying to understand the evolution of the gut microbiome. We know that the communities of bacteria that live in our gut are highly responsive to the diets that we eat. And we know that industrialized diets have really changed the way that our microbial communities are structured.

And in many ways, these changes are associated with health consequences and chronic inflammation. So the big question we wanted to ask was, historically or pre-historically, when did these changes start to happen? Is it really associated with industrialization? Or might it begin earlier with more intensive agriculture, or maybe with the beginnings of agriculture?

So part of what we were trying to do was to look for human feces from different points in time and try to understand how it had changed in response to different new human social behaviors. What we found along the way was also all the dog poop mixed in.

So part of this study was coming up with a systematic way of separating those so that we could focus on the human feces and understand this evolutionary process. But then, it also gave us a new window into dogs, which are some of our oldest friends. And how they have adapted and lived alongside us over the same period of time.

KATHLEEN DAVIS: And what did you find that might shed more light on that?

CHRISTINA WARINNER: So that is the focus of a study that we’re still doing. I mean, we found some basic information. So, for example, from the human feces, we’re able to reconstruct aspects of information about those individuals. We could tell if they were male or female. We could reconstruct their ancestry profile and show that it matched the region of the world that they came from.

We also were able to identify some of the dietary components. So, for example, from the individuals from northern Mexico, we recovered a lot of maize DNA and also some other DNA of plants that are very common in traditional rural diets. And so we were able to reconstruct some of that information.

Our next step now is trying to understand how these microbial communities have systematically shifted in response to things like social complexity, new forms of agriculture, state-level societies. These are some of our interests.

KATHLEEN DAVIS: I’m curious, do you have a favorite coprolite that you’ve studied?

CHRISTINA WARINNER: Of course I do. So I work at both ends of the gastrointestinal tract. So I work on coprolites, which is paleo feces, and I also work on dental calculus, which is calcified dental plaque. So all the things that people spend money trying to get rid of I’m so interested in. And I definitely have favorites. There’s some that we’ve found that we’ve just found really fascinating information from.

So I have to admit the dog coprolite from the chamber pot was quite the puzzle for our whole group. It took us a lot of time working out what might have happened there. And so that was a really fun project to work on. We also have looked at other individuals, that are not included in this study, who just had a really wide variety of foods and are giving us a tremendous insight into whole meals that people consumed thousands of years ago.

So those are some of the really exciting samples to work on.

KATHLEEN DAVIS: I’m Kathleen Davis, and this is Science Friday from WNYC Studios. We’re talking to Dr. Christina Warriner, an assistant professor of anthropology at Harvard University in Cambridge, Massachusetts.

So you mentioned that you work at both ends of the gastrointestinal tract. Tell us a little bit about studying fossilized plaque. What can you learn from that that might be a little bit different than studying coprolites?

CHRISTINA WARINNER: Yeah, so coprolites are fantastic in terms of the range of information you can get from them, but they’re rare. So we can only really access particular places and times in the past. What’s really exciting about looking at calcified dental plaque, or calculus, is that nearly every skeleton has it. And so this really opens up the entire archaeological record for us to investigate the past.

One thing that people go to their dental hygienist, to the dentists, and they have all of their calculus, or their tartar is another term for it, scraped away. But it’s a really amazing material. It’s the only part of your body that actually fossilizes while you’re still alive. And it’s the sticky substance that slowly calcifies, and during that process, traps all sorts of debris related to your daily life.

So we find everything from seasonal pollen that gets trapped in. Was probably an allergen. We find little bits of tiny fragments of food. So plant microfossils getting trapped in calculus. We find, of course, bacteria that are present. We find human DNA. Also we find a lot of dietary proteins. And so this is a technique that we’ve been really exploring lately in reconstructing the food histories of different places by looking at the food proteins that get left behind and entrapped in this calcifying dental plaque.

And in particular, we’ve really focused on using this to track the origins and spread of dairying around the world, which originates in the near east about maybe 9,000 years ago. And then, spreads from there to Europe, Africa, and throughout Asia.

KATHLEEN DAVIS: Speaking of dairy, food allergies and intolerances are pretty common these days. Can we learn about things like lactose intolerance from studying these fossilized feces and plaque?

CHRISTINA WARINNER: Yes, and I think this is something that is really exciting. This is something my group is working on right now. Lactose intolerance is actually a really interesting phenomenon. On the one hand, all mammals produce lactase, which is the enzyme we use to break down the milk sugar lactose. And we produce this in our small intestine, and it helps us to digest milk when we’re young, when we’re infants.

But all mammals are actually genetically programmed to lose the ability to produce this enzyme effectively becoming lactose intolerant. And this is part of the weaning process of mammals. And what’s really interesting in humans is that a subset of humans have developed mutations in the system such that they just produce lactase all the time and for their entire lives.

These mutations are in Europe, parts of the near east, and parts of East Africa. And so these populations are called lactase persistent. And they’re milk tolerant. But what’s really interesting is that we see that while these societies in these areas have long practiced dairy production, we also see that other populations, for example, in Mongolia, also have very long histories of dairying.

And this is something we’ve shown through some of our work looking at preserved proteins in dental calculus. We can trace back the origins of dairying in Mongolia more than 5,000 years. What’s really amazing about Mongolia today is that they milk seven different species of animals. So they milk cattle, sheep, goats, yaks, horses, camels, and reindeer.

And yet, they don’t have any of these mutations that are associated with producing lactase. So this has long been a puzzle that these mutations don’t actually explain all of the dairying behavior that we see in populations around the world. So we’ve been working really closely with herders in Mongolia trying to understand this. And we are starting to gather evidence that we think that the microbiome is really strongly involved in this process.

KATHLEEN DAVIS: That’s so interesting. Dr. Christina Warriner, that’s all the time we have for today. Thank you so much for joining us on Science Friday.

CHRISTINA WARINNER: Thank you.

IRA FLATOW: That was sci-fi producer Kathleen Davis speaking with Dr. Christina Warriner, assistant professor of anthropology at Harvard University.

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